gentoo-overlay/sci-biology/infernal/files/infernal-1.0.2-fix-build-system.patch

* Fix parallel build
* Respect AR
* Respect DESTDIR
* Respect LDFLAGS

--- a/easel/Makefile.in
+++ b/easel/Makefile.in
@@ -17,7 +17,6 @@
 #
 CC       = @CC@
 CFLAGS   = @CFLAGS@
-AR       = @AR@ rcv
 LN       = ln
 RANLIB   = @RANLIB@
 LDFLAGS  = -static @LDFLAGS@
@@ -132,13 +131,13 @@
 	esl_wuss.o
 
 all: libeasel.a
-	(cd miniapps; make)
+	$(MAKE) -C miniapps
 
 .c.o: 
 	${CC} -I. ${CFLAGS} ${SIMDFLAGS} ${DEFS} -c $<		
 
 libeasel.a: $(OBJS)
-	$(AR) libeasel.a $(OBJS)
+	$(AR) rcv libeasel.a $(OBJS)
 	$(RANLIB) libeasel.a
 	chmod 644 libeasel.a
 
--- a/easel/testsuite/Makefile.in
+++ b/easel/testsuite/Makefile.in
@@ -15,7 +15,6 @@
 LIBS     = @LIBGSL@ @LIBS@ -lm
 MPILIBS  = @MPILIBS@
 
-AR      = @AR@ rcv
 RANLIB  = @RANLIB@
 
 ESLDIR = ..
--- a/iinfernal-1/Makefile.in
+++ b/iinfernal-1/Makefile.in
@@ -20,7 +20,6 @@
 #  only used for building the testsuite anyway... e.g. we
 #  make a "libhmmer.a" library for building the testsuite.
 #
-AR     = @AR@ rcv 
 RANLIB = @RANLIB@
 
 MPILIBS   = @MPILIBS@
@@ -63,7 +62,7 @@
 module: libinfernal.a
 
 libinfernal.a: $(OBJS) 
-	$(AR) libinfernal.a $(OBJS) 
+	$(AR) rcv libinfernal.a $(OBJS) 
 	$(RANLIB) libinfernal.a
 	chmod 644 libinfernal.a
 
--- a/Makefile.in
+++ b/Makefile.in
@@ -82,9 +82,10 @@
 all: core 
 
 core:
-	(cd easel;     make CC="$(CC)" CFLAGS="$(CFLAGS)"; make)
-	(cd src;       make CC="$(CC)" CFLAGS="$(CFLAGS)"; make module)
-	(cd testsuite; make CC="$(CC)" CFLAGS="$(CFLAGS)")
+	$(MAKE) -C easel
+	$(MAKE) -C src 
+	$(MAKE) -C src module
+	$(MAKE) -C testsuite
 
 #.PHONY: $(RIGFILTERS)
 #$(RIGFILTERS): core
@@ -202,9 +203,9 @@
 # "make install" installs the programs in BINDIR
 #
 install:
-	mkdir -p ${BINDIR}
+	mkdir -p $(DESTDIR)${BINDIR}
 	for file in $(PROGS); do\
-		cp src/$$file $(BINDIR)/;\
+		cp src/$$file $(DESTDIR)$(BINDIR)/;\
 	done
 #	if test -d $(RIGFILTERS); then\
 #	   for file in $(RFPROGS); do\
--- a/rigfilters/cfsqp/Makefile.in
+++ b/rigfilters/cfsqp/Makefile.in
@@ -24,7 +24,6 @@
 ## archiving command, and ranlib command.
 # these are used to create the libcfsqp.a library, necessary for cm2hmm
 #
-AR     = @AR@ rcv 
 RANLIB = @RANLIB@
 
 OBJS  = cfsqp.o\
@@ -41,7 +40,7 @@
 all: libcfsqp.a
 
 libcfsqp.a: $(OBJS) ${HDRS}
-	$(AR) libcfsqp.a $(OBJS) 
+	$(AR) rcv libcfsqp.a $(OBJS)
 	$(RANLIB) libcfsqp.a
 	chmod 644 libcfsqp.a
 
--- a/src/Makefile.in
+++ b/src/Makefile.in
@@ -27,7 +27,6 @@
 #  only used for building the testsuite anyway... e.g. we
 #  make a "libinfernal.a" library for building the testsuite.
 #
-AR     = @AR@ rcv 
 RANLIB = @RANLIB@
 
 # configuration for optional MPI functionality
@@ -86,7 +85,7 @@
 all: 	$(PROGS) 
 
 $(PROGS): @EXEC_DEPENDENCY@ $(OBJS) ${HDRS}
-	$(CC) $(CFLAGS) $(DEFS) $(MYLIBDIR) -o $@ $@.o $(OBJS) $(MYLIBS) $(LIBS) $(MPILIBS)
+	$(CC) $(LDFLAGS) $(CFLAGS) $(DEFS) $(MYLIBDIR) -o $@ $@.o $(OBJS) $(MYLIBS) $(LIBS) $(MPILIBS)
 
 
 #################################################################
@@ -95,7 +94,7 @@
 module: libinfernal.a
 
 libinfernal.a: $(OBJS) ${HDRS}
-	$(AR) libinfernal.a $(OBJS) 
+	$(AR) rcv libinfernal.a $(OBJS)
 	$(RANLIB) libinfernal.a
 	chmod 644 libinfernal.a